Emerging from Deep Waters
by Peachy Momiji
Summary: After the in many ways rather vague ending of the season 4 finale, a very special conversation cannot be missed out, however. It is the one between Molly and Sherlock about what happened, what the consequences might be and how to live with, learn from and grow through all those experiences.


**Well then, I could not resist to write down some ideas concerning 'The Final Problem' either. The story just turned out to be a bit longer than even I, myself, expected it to get.**

 **I do not own any of the characters.**

 **Please enjoy!**

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 **Emerging from Deep Waters**

It was gloomy outside. A dark and harsh landscape slowly being illuminated by the first signs of a new day rising.

Within a day, _any_ day, everything seemed to be possible. One could simply spend it with work, with friends or family, in one's mind palace, all at a very slow pace. One could also lose something, a job, a person, maybe sanity.

One could also gain a lot of things within a day. A lost toy, memories, even a person. For all he knew, the world could go down in less than a day. What came after that, if there would even be an 'after'... well, that was one of the, as he began to realise, many things he didn't know these days. Being uncertain wasn't something he particularly enjoyed. It actually was scratching his mind open. However, he also realised that it was a major part of being _human,_ which was a fact about him he had been rather forcefully faced with during the past few weeks. He would have to learn to just live with it.

Yesterday had been one of these days, where quite literally _everything_ happened to and through him.

He won back his sister, the memories of his best friend, his _life_ and personality before it had reached its pivot point so very early in his childhood... and realised actually what he had lost all those years ago. What he missed out on doing due to his lack of memory, that he brought upon himself in the first place. He realised the actual _loss_ and trauma he had been faced with back then and just again yesterday by witnessing lives being destroyed, people being killed, him and his brother and his best friend being toyed with and tormented. And all the while he was actually forced to be a part of it all, to be the one harming others. People he didn't know at all and, even worse, people he appreciated and cared about greatly. All the pain, all the fear, anger and desperation... it was exhausting.

These were the turbulent thoughts of the infamous London detective, Sherlock Holmes, as he was on his way back home after one day and night that would prove to be another pivot point in his very life.

While Sherlock's thoughts were lost at a stormy place, John's mind, however, had been occupied by only one person: Rosie, his little daughter, that he almost had left alone for good.

But they were safe now, all of them. He had to remind himself over and over of that very fact. And John would rather die than let his wife down and forfeit to take care of their daughter, as he had promised to Mary and to himself. He would make it up to Rosie, that was for sure.

But he was more than a father and a husband. John Watson was also a friend, a best friend to the person he knew was in a lot of pain and faced with way too many revelations a normal person could usually handle all at once. However, Sherlock Holmes wasn't _any_ person and the situation was being far from usual. He would turn towards his friend and ask him anyway,

"So... what exactly is the plan from now on?"

Sherlock stopped his thinking for just a second to ponder his answer. He finally said with the fatigue evident in his voice,

"Picking up the pieces and then see how to move on from there, I suppose."

The truth was, he had already made a list in his head.

Making sure Mycroft was okay, talking with his parents and contacting Victor's parents, the Trevors, upon their son's tragic fate were definitely at the top of it... all that and making amends towards the person he probably hurt the most during this horrific process wanting to make sure she would be okay.

Restoring his flat and possibly trying to reach out to his sister would come right after thought undertakings.

John, as though reading his mind just asked, "And what's the first priority then?"

Without hesitation the answer was, "Talking to Molly Hooper." He added, "After all, the cameras need to be removed first. "

On that John frowned and asked quizzically, "Wait, you are not going to talk to her _now_ , are you?"

Without a doubt in his voice Sherlock said, "Of course I will. There is no room for postponing it."

"Well, I like that you feel about it that way, Sherlock, but don't you think, well... that you should just give her some more time to calm down and process everything? Just let Mycroft's people handle the cameras."

"They won't. I have already texted Mycroft to leave Molly Hooper alone." "Why would-" "It is my fault, John. Everything." Sherlock answered with the utmost seriousness as he turned to look his friend in the eye, "I have to be the one to make it right. It is my responsibility. That shouldn't be done by anyone else."

John took that information in and just said quietly, "Of course that's true, but... maybe there is no way to actually make it _right_ again. Sometimes things are just changing, which is inevitable at a certain point. And we need to change with them in order not to be left behind." The image of Mary appeared in his head as soon as he had said it.

"I know." Sherlock responded with a slight tone of resignation, that wasn't missed by the doctor, however.

"What is it?"

"I simply don't know whether it is going to change for the better or the worse and that frightens me the most." was the detective's honest response. He knew he had to be truthful about the feelings he held inside him in order to properly convey them to the people that were dear to him, which wasn't hard at all with John, not any more at least. That was one of the first realisations that hit him once he had learned to deal with something as complicated and sometimes vicious as emotions. And he had to do the same once approaching Molly in order to make that conversation work.

John nodded compassionately, understanding his friend's concerns. He answered, "You'll never know for sure, but you'll always have to try."

Sherlock processed that statement and found himself believing it was true. The conversation was over, just until the car finally stopped by Molly's little house. Both of them were not eager to talk much, for they first needed to rest their minds and think things through, especially Sherlock. John decided it wouldn't be wise to bother his friend further with more questions about what he was actually feeling towards Molly and how exactly he planned to explain everything to her. He didn't even think Sherlock was sure about that himself just yet. But he trusted his friend. He trusted that he would eventually find the right words to say and whatever the detective had learned about himself during the past ordeal, however much he had suffered in order to come out of it alive, John had to admit that he was damn proud of him. For the doctor knew just how much more his friend could grow in character now that so many pieces had been put together. He chose to leave it at that for now.

John gave his friend an encouraging look once they had reached their destination. "Good luck, mate. I'll see you later." Nodding and with resolve and determination in his features, Sherlock walked into the cold towards Molly's door.

It was about half past five in the morning and Molly was lying on her couch. She had fallen asleep there sometime in the middle of the night... after a bottle of red wine and a long conversation with her mother who she had called again (after weeks of not talking to her at all) over her misery.

The relationship she had with her mum wasn't at its peak, she had to admit that to herself. They were much too similar in her eyes and after her father, the one person who was able to even everything out between them due to his calm and conciliatory nature, had died every conversation between her and her mother seemed to hurt a little bit more, seemed to set both of them a little bit more on edge and that didn't appear to help anyone.

As a consequence the contact became rarer, their bond more distant, although the voice of reason in the very back of her mind told her that avoiding her mother wouldn't solve anything. In the end it would just leave her more lonely than she would have ever liked to admit she was.

Yesterday, however, had been a different case.

She had felt like being punched and then left alone bleeding without anybody caring.

She had felt so lost, just as though she was drowning.

She had felt like as though she didn't matter to anyone anymore.

In such a situation you turn to the ones who have always been there for you and always would be. The ones who always loved you, no matter what happened along the way. So did Molly. She had a three-hour tearful, heart wrenching phone call with her mum, which – as she actually had the feeling – was at least the beginning of healing their relationship.

They had talked about everything... Sherlock and all the years of their developing friendship from Molly first merely having a crush on him up until the phone call, where the actual depth of her feelings had finally been revealed. They talked about Mary and Molly's role as being a godmother to her friends' daughter Rosie and how hard it lately had been for her to reconcile being a pathologist and also a pillar in the lives of the people most dear to her. They even talked about her dad and had quite a good time recalling the most pleasant and dear memories with him.

The way Molly and her mother alike were laughing as well as crying over something they shared together really did work wonders on getting her mind off the rather heart breaking occurrences that had taken place during the past months.

Molly had finally been able to fall into a deep (partly wine induced) sleep with the pleasant anticipation of seeing her mother again very soon.

That was until she woke at the inhumanly early time of 5.30 a.m. due to a firm knocking on her door.

She rubbed her eyes and got up to open it. For a moment she couldn't even remember what had happened the other day due to her sleepiness. However, that condition changed quickly once she stared up into the face of the one and only Sherlock Holmes. And it all came crushing back down at her.

The phone call. The confession. The tears.

And her first reaction was to slam the door shut again. She didn't want to see him. In that moment she didn't feel like ever wanting to see him again.

Sherlock, however, was faster than her and stopped her from shutting him out like that by placing a hand on the door. "Please don't!" he said with slight desperation audible, willing her to take a closer look at him.

Following his gesture she felt the urge to yell at him just to leave her alone, but once she actually did take a second look, her mouth came to a halt without any words escaping it.

Molly stared at a man she had problems recognizing as the same Sherlock Holmes she used to know. The man on her door step was different... physically dishevelled and bruised with the lack of sleep evident in every part of his whole shape. However, that wasn't what stunned her the most.

It was his whole demeanour. The way his shoulders were sagged down. The way he barely seemed to be able to stand straight and steadily. The way he looked at her, with an exhausted and broken and unutterably sad expression, beyond anything she ever saw in him pleading with her not to close the door.

She realised slowly then that he actually was at a loss for words. Something that rarely ever happened to the most brilliant and talented detective the world had ever seen... unless something truly severe had happened.

And it hit her right then and there.

She cared and she always would. After all, she _did_ love him, for unlike him she had been honest when she said she did. She loved him for _who_ he was. With all his talents and his flaws, because he was Sherlock Holmes, the gifted, witty, unequalledly intelligent, very often infuriating, but always being concerned about his friends detective who never did anything without a reason... a phone call couldn't change all that.

The way he felt about her did not define him as a person, it never would and she wouldn't want that even if he did return her feelings. Therefore she couldn't be indifferent towards him and his problems.

She might have hated him at that moment for everything he had put her through, seemingly without a care or second thought about what that did to her.

But those feelings could not erase the picture of a man Molly had been able to recognise in Sherlock years ago, maybe since John Watson had entered his life. A picture so unlike the 'high functioning sociopath' he was trying to fool everyone, including himself, to believe in. In her mind's eye he was the man who had grown so much into becoming the good person he was capable of being.

The man who had given the most unorthodox, yet adorable wedding speech a best man could have ever delivered.

The man who had become a godfather to the sweetest little girl Molly had ever known.

The man who tried his very best to protect the people he held dear, even if it meant putting his own life on the line due to that cause.

The man who trusted her once... more than anyone else.

Despite the turmoil of feelings that threatened to swallow her whole, Molly also realised that she wasn't defined by them either. She was Molly Hooper, after all. The hardworking and always engaged pathologist, the cheery little woman who tried her best to lighten the day of the people in her life, when everything surrounding them was nothing but gloominess, the only daughter to her parents, the friend who was never able to stop caring, when somebody was in need of her help.

One phone call, one rejection, one humiliation more couldn't change that.

As for now she could tell that something was definitely very wrong and something very bad had happened to Sherlock. A part of her wasn't surprised at all about it, especially since she had recalled that some inner voice of hers had already told her yesterday that something was off about him during this completely contextless, strained phone call.

And since he also owed her a very explicit explanation, she stepped aside and let him enter her house.

Relief started to flood his features. He came him and, unlike everything Molly would have expected him to do, he entered her living room looking around frantically.

In his mind he was measuring ankles and distances trying to detect the exact locations of the cameras that had been placed there by his sister. It didn't take him very long to find and remove them.

After that was done he started to ramble through the house in search for more observation material and he found several cameras in each room. Sherlock had already expected that much, since it was simply impossible for Euros to predict the room Molly would have been in, when _the call_ had been made.

All the while Molly just stared incredulously at the growing amount of cameras piling up on the desk before her. She was completely taken aback and already exhausted from the encountering with Sherlock even before they had exchanged more than three words.

When he was finally done and convinced he had removed all unwelcome devices he paused in the middle of the living room, heavy breaths escaping from his mouth.

Molly, however, started to lose her nerve again, along with the sorry rest of her patience. She was completely pissed off and almost didn't manage to keep the anger from showing in her voice as she pointed towards the cameras, a constant frown now gracing her features, "Well? Any explanation?"

When he didn't give an immediate answer, she went on furiously, "Sherlock, seriously? You cannot just come here after everything that happened _yesterday_ , pull out half the equipment of our secret service and not explain anything, you simply can't! I mean, what were you expecting? That I would be okay with all of this? You've got to do better than that!"

To make a point she wrapped her arms tighter around herself than she already had. She wouldn't be easy on him, not today.

"Molly..." he said with his voice even lower than usual. Now he would reach the hard part of his visit. Unable to face her, he stared to the ground at her feet, aware of her critical gaze which lingered upon him. Breathing in deeply he finally lifted his head, defeat as well as determination filling his facial expressions. He could do this, he had to.

"Whatever it is that you might think about me, that you might think you already know about me or that you are going to learn about me, please know..." She was holding his gaze expectantly. He sighed once again and closed his eyes for a brief moment, then he continued, "Please just know that I am most glad and overly relieved that you are save and well and that everything I did and everything I said was just to keep you from harm, although I am more than aware of the damage I have caused during the process."

He swallowed hard, so did Molly. While fighting her own tears at the memory of their last conversation, she cleared her throat and said, "Well then, I am all ears."

"It actually is quite a long story..." he added.

"Then why don't you just start at the beginning? And while you're at it, please have a seat before you're collapsing right there on my floor, for you look like you might do that at any moment." Molly responded with some concern in her voice.

As she slowly approached Sherlock and tried to lead him to her couch, she could feel some of the tension that held his body upright leaving and was even more afraid he might truly faint. Sherlock was merely thankful she was still offering her help in that way. It gave him hope that he hadn't lost her and the pieces of what was left of their friendship for good, which had been his biggest fear to begin with at that moment.

When they were finally seated facing each other again with steaming cups of tea by then, Molly was so kind to lead the detective back towards the subject at hand, since she could tell he was now having trouble focusing. "So, the beginning it is. What happened to you yesterday?"  
To that, Sherlock just gave a mirthless chuckle, "Yesterday? Oh, it didn't start yesterday..." Bracing himself for what was to come, he then continued, "As you may not know... I have a little sister. A sister I, myself, did not have any memories of up until yesterday, however."

The information hung in the air like mist and none of them said anything. Molly never broke eye contact and connoted that she wouldn't interrupt him. He needed to get, whatever this story of his was about, off his chest and she would just sit there and listen to him, just like she had offered to do years ago on that fateful evening at the lab.

After all, a secret sister wasn't the most dreadful information about Sherlock that had ever been revealed to her.

He, however, wasn't able to keep looking her in the eyes. Instead he kept talking to his tea pot,

"When I was six years old I had a best friend whose name was Victor Trevor..."

And so he told Molly everything he remembered learning about himself during the last 24 hours. About Redbeard and their adventures as pirates, his genius little sister Euros being the cause of his sudden disappearance and finally his death, Sherlock's previous home going up in flames and his overchallenged childlike mind not being able to cope with all of those tragic events, so it invented a less hurtful story and erased his sister along with it. He talked about Euros conspiring with Moriarty and their devious plan about destroying Sherlock Holmes, when all his sister wanted was to finally be noticed by him... and saved. He told her about the hell he, his brother and John went through in Sherrinford, his sister's sick little mind games and the showdown at the old Holmes' residence, where he had finally been able to turn tables, solve an almost forgotten riddle and save not only John, but also the 'girl on the plane'.

All the while Molly Hooper realised things about Sherlock she hadn't noticed earlier. He was in shock, clearly. The way he was conveying all these highly emotional occurrences and the psychological trauma that inevitably came along with it to her with such an even and monotonous voice... He was isolating himself from everything that had happened in order to tell her the whole story, just like he and John had done earlier by claiming to be 'soldiers' in order to survive each and every ordeal. It all made perfect sense. The thing was, it was over now. He did not have to distance himself anymore. Molly made a mental note to come back to that topic, when he would be finished.

When telling the woman in front of him about the circumstances of the phone call and the coffin, he didn't leave out one detail and forced himself to look her in the eye during that part. She deserved to know everything about it after all.

"Look, I know that this might be unfair to you... me telling you the whole story with all its tragic events, since I don't want you to be manipulated into being forgiving just because you are feeling sorry for me or because you think you ought to be grateful for me saving your life which, however, wasn't in danger in the first place." he said in a husky voice, giving her the most intent stare Sherlock Holmes could ever muster.

Molly's eyes started to fill with tears and she looked away. The man sitting opposite of her, clearly having some trouble finding his next words, went on, "But I want you to know..." he tried and failed to steady his trembling voice, "...that I am really, truly, utterly sorry that you got caught in the middle of the crossfire, and that I was the one to hurt you this profoundly. You didn't deserve any of that, you of all the people who matter the most to me. I have always been able to rely on you."

A few tears had fled Molly's eyes, leaving soft traces of moisture on her cheeks while Sherlock did not stop studying her.

"Molly Hooper, I know that I am again asking too much of you, but please dare to put your trust in me just one more time. And I promise to give my very best never to harm it again and I will vow to treasure our friendship the way it truly deserves to be treasured. I am telling you all of this, because I really would give anything to keep you as this close a friend, not because I need you as my pathologist, but because I want you, all of you, in my life and I – "

Holding up a hand this was the first time Molly interrupted Sherlock's monologue. "Just hold on for a moment... what do you mean by 'all of me'? What are you trying to say?"

He rarely ever spoke of her in such a way and she was not used to him opening up about his emotions with such generosity. After the phone call she had told herself he did not mean what she had made him say and up to this point everything Sherlock had said proved her to be right. She could not afford to even get her tiniest hopes up that he might have been in even the slightest way sincere about it. Her heart would not survive it, that much she knew.

Sighing, Sherlock once again turned his attention towards his tea cup. He finally answered, "Look, I am not very good at this kind of conversation... for all my life I have kept telling myself that having, expressing, being concerned with sentiment would be an inconvenience all by itself, doing nothing but slowing me down. And today I found out that all of this was a complete lie. That the only reason I avoided emotions as forceful as I could was, because I did not want to get hurt."

Taking a steadying breath, Molly reached out towards Sherlock's hand and said, "But you cannot stay where you are now forever. You have learned a lot about yourself during the last couple of hours and why your mind works the way it does and why your heart feels the way it does... try to take it as a gift, in spite of the loss you have also discovered along the way." she gave him another meaningful look, "and try to become better and stronger because of it. Even when you say you have issues dealing with feelings... that is something you need to practice, just like learning to play the violin. It is not always easy and I can assure you that you will get hurt and hurt others along the way, but it will be worth the pain. I can promise you that much. And you can finally become the man you choose to be out of your own free will, without being manipulated by Mycroft or Euros or Moriarty, the man who is not only brilliant at what he does, but also kind and protective towards all the people he cares about and to that... well, I am really looking forward to that."

Molly was now smiling, despite the tears gracing her face and Sherlock just stared back at her, completely amazed. Shaking his head, he said, "You're really unbelievable..."

"What do mean?" she questioned him confused.

"I... I really did not plan on telling you this right now, not before I would have found some way to prove it to myself, but... well, whereas I might be oblivious to people's feelings and my own on many occasions, although I might add that I have already gotten better at that part, I rather dedicated my life mainly towards finding out the truth in riddles and expose mendacity once it has been discovered."

Molly, anticipating where this might be going, drew back carefully, holding her breath as Sherlock started to speak again, "And during that phone call, while I said what I said to you –"

"Please don't –"

"It didn't feel like a lie." he finished despite her interjection, as ponderous silence followed that statement.

"Why are you doing this to me again?" Molly responded breathlessly.

"Please just listen to me, Molly... I don't want to hurt you. In fact, when I did, when I had to do it, it felt like I had broken something very precious inside of myself that was so tiny and fragile, I hadn't even realised it was there before. That is why I was foaming with rage in such an uncontrollable way. And all the pain... I could not place it anywhere. I wanted to find out now in the aftermath what the meaning of all of this had been, since I am not very familiar with romantic love and... well, I think I just did."

He looked at her hopefully, but she didn't understand a thing about what he had said. After all these years of rejected feelings and the phone call being the final straw, she just couldn't believe him telling her the complete opposite now.

Sherlock went on nevertheless. He had to end what he had begun, no matter how emotionally draining it was for him being this open with her. After all, she was the person _who mattered the most_.

"To be honest, I am nobody near the man that you deserve to have in your life, that is quite certain. And although I have been aware of your affections towards me right from the beginning, it has always been alien to me why you were feeling that way, since I had nothing to give you in return. I was quite empty." he told her with a said smile. Once again he looked to be very broken in Molly's eyes.

"There is no reason 'why' you are feeling the way you feel. It does not always make sense." she offered silently looking towards the ground.

"I know. But for a long time I did not believe to be capable of loving, well, anyone."

"Not even yourself?" Molly said making eye contact again, which Sherlock broke this time. Memories of self-destructive drug abuse and even more severe withdrawal procedures entered their minds' shared space.

"Not even that, I'm afraid." he answered with a slightly wavering voice, "At least not until I made friends with John Watson, who gave me some very important advise lately. And I am more than glad that I, unlike him, have the chance to say this to you while being face to face. And I won't miss it."

He did not quite understand why he was getting overly emotional all of a sudden or why his eyes were starting to get moist or why he didn't seem to be able to keep his tone in check properly or why he started to develop a slight tremor that overtook his whole body...

Maybe it was the lack of sleep, the destruction of the rather peaceful picture of his childhood with his sister and his best friend gone, the trauma of Sherrinford or the fear for John's and Molly's and Mycroft's lives... probably it was the amount of it combined that he could not shoulder any longer.

"Molly Hooper, you have been able to see through me, to see the real me and to love me for that, despite the flaws which come along with that image. And this precise image would never be enough to deserve your love. However, the picture you have of me is nothing but an illusion. It is not the real me. For the person you see in me is the person I want to be. And the man you think I could become, what you mentioned earlier..." he added with an unmistakeable tremble in his deep voice, " ...this man would try his very best to give you all the love you deserve, all the love he did not dare to recognise and left hidden at a very dark and lonely place before.

That is a possibility for the future, I can see it clearly. But only if you are still willing to give me another chance first, if your feelings haven't changed already."

It was enough for Molly. It was all she had ever wanted, him being honest, being open with her, being _Sherlock_. After all this time, when _she_ was the one being in love with _him_ , _he_ was asking _her_ to give _him_ , to give _them_ a chance. Beautiful irony.

As he was now rubbing his eyes furiously, cursing himself silently for not even being able to keep it together until she gave him an answer, he felt her moving next to him, wrapping her arms around him and giving him the opportunity to rest his head on her shoulder.

"You _are_ an idiot. For you know I have been truthful, when I said that I loved you. And I actually begin to think that this is never going to change. You do not get to choose who you love, Sherlock, for better or for worse." Molly reminded the man in her arms with a soothing voice, trying to ease away all the tension that still kept his mind and body on edge as she stroked his curly hair with one hand and his back with the other one.

"And I also want you to know that it is because of the love you held and still hold for your friend, as well as for your sister, despite everything she had done to you, that you became who you are today. Inventing a less painful story to keep you from accepting the fact that a loved one was responsible for the death of another person which was very dear to you as well is just a consequence of that unyielding love of yours. It was probably the only way you could have survived such trauma back then."

"And that meant completely forgetting about them, just like they never existed?" he choked out, finally holding onto Molly as well. She hugged him even tighter to emphasize her next statement.

"What is important is that you can remember _now_. You can finally find closure and allow yourself to mourn, because you don't have to feel alone anymore, never again. You have me and John and Rosie and your brother and we are all alive, we are save. _You_ have kept us save.  
And you cannot blame yourself for what had happened in the past, since you were just a little boy, who wasn't ready to face his sister's demons and his friend's departure yet."

"But I can do now." was all Sherlock managed to say when he buried his face into Molly's shoulder as heavy sobs began to shake his body and let himself experience a completely different emotion of equal importance: grief.

Grief for all that he had to go through first in order to be able to become the very best of himself, to a large amount for the woman who would never let him face his very own demons all by himself.

 **The End**

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 **Hoping you enjoyed reading this story I would be very grateful for any kind of feedback, may it be positive or negative!**

 **I would also like to thank a very good friend of mine who was so very kind to help me correcting some of the grammatical and orthographical insecurities of this story, since English is not my mother tongue.**

 **Have a wonderful week!**


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